1) It would indeed be better to replace to whole frame rail. They make full rear frame rails that include the torque boxes and they are pretty much easy to replace and you have a rotisserie so it will be twice the fun. IF the current torque boxes AND shackle ends are shot you can pretty much gurantee rust is throughout the entire rail.
2) It IS easier to remove wheel wells to get to everything. Trunk drop-offs probably need to be replaced to so just take it all off.
3) It is easier to get to the rear of the frame rails with the tailight panel off.
What helped me was doing one side at a time to keep everything square. I recommend this. You don't want to put the rear axle back on and find you are driving sideways. As you make your tacks to the trunk floor before final assembly please keep checking your squared using the other frame rail as a reference point. Take measurements before you remove anything. If helps to plumb-bomb mounting points to the floor and make marks on the floor to help keep things lined up.
"yeah though I walk through the valley of the shadow of rice, I will fear no turbo for torque art with me. Thy rods and thy crankshaft, they comfort me."
1965 Fastback 289 hi-po 3sp.
1973 coupe 302 4V auto. -SOLD
1965 coupe 200 I6 (bench seat option)